Experiment set2IT047 for Agrobacterium fabrum C58

D-Galacturonic Acid monohydrate carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + D-Galacturonic Acid monohydrate (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 10/20/20
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 59 genes in this experiment

For carbon source D-Galacturonic Acid monohydrate in Agrobacterium fabrum C58

For carbon source D-Galacturonic Acid monohydrate across organisms

SEED Subsystems

Subsystem	#Specific
Flagellum	7
D-Galacturonate and D-Glucuronate Utilization	4
Flagellar motility	3
Ammonia assimilation	2
Branched-Chain Amino Acid Biosynthesis	2
D-galactarate, D-glucarate and D-glycerate catabolism	2
Homogentisate pathway of aromatic compound degradation	2
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Acetoin, butanediol metabolism	1
Alanine biosynthesis	1
Anaerobic respiratory reductases	1
Arsenic resistance	1
Bacterial Chemotaxis	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Biogenesis of cytochrome c oxidases	1
Catechol branch of beta-ketoadipate pathway	1
Chitin and N-acetylglucosamine utilization	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Flagellum in Campylobacter	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutamine synthetases	1
Glycogen metabolism	1
L-rhamnose utilization	1
Mannitol Utilization	1
Peptidoglycan Biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Sialic Acid Metabolism	1
Terminal cytochrome C oxidases	1
Trehalose Biosynthesis	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine biosynthesis
• Nucleotide sugars metabolism
• Butanoate metabolism
• Pantothenate and CoA biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Fatty acid biosynthesis
• C21-Steroid hormone metabolism
• Oxidative phosphorylation
• Puromycin biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Bisphenol A degradation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Starch and sucrose metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• C5-Branched dibasic acid metabolism
• Carbon fixation in photosynthetic organisms
• Thiamine metabolism
• Atrazine degradation
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
urea degradation I	3	3	3
L-alanine biosynthesis III	1	1	1
L-cysteine degradation IV	1	1	1
L-glutamine biosynthesis I	1	1	1
D-galacturonate degradation II	5	5	4
D-glucuronate degradation II	5	5	3
L-valine biosynthesis	4	4	2
D-glucuronate degradation III	2	2	1
ammonia assimilation cycle I	2	2	1
superpathway of allantoin degradation in yeast	6	3	3
cytidylyl molybdenum cofactor sulfurylation	2	1	1
ammonia assimilation cycle II	2	1	1
arsenate detoxification III	2	1	1
pyruvate fermentation to (R)-acetoin II	2	1	1
arsenite to oxygen electron transfer	2	1	1
D-galacturonate degradation III	2	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	2
cyanuric acid degradation II	5	3	2
cyanuric acid degradation I	5	2	2
pyruvate fermentation to (R)-acetoin I	3	3	1
D-glucarate degradation II	3	3	1
L-citrulline degradation	3	3	1
ammonia assimilation cycle III	3	3	1
D-galactarate degradation II	3	3	1
cyanate degradation	3	2	1
pyruvate fermentation to (S)-acetoin	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
L-isoleucine biosynthesis IV	6	3	2
arsenite to oxygen electron transfer (via azurin)	3	1	1
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	2
L-isoleucine biosynthesis III	7	4	2
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
thiazole component of thiamine diphosphate biosynthesis II	7	4	2
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
biotin-carboxyl carrier protein assembly	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
L-arginine degradation V (arginine deiminase pathway)	4	3	1
L-isoleucine biosynthesis II	8	5	2
2-deoxy-D-glucose 6-phosphate degradation	4	2	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
arsenic detoxification (bacteria)	4	2	1
superpathway of atrazine degradation	8	3	2
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
glycogen biosynthesis II (from UDP-D-Glucose)	4	1	1
superpathway of branched chain amino acid biosynthesis	17	17	4
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	22	7
chorismate biosynthesis from 3-dehydroquinate	5	5	1
uracil degradation III	5	5	1
4-deoxy-L-threo-hex-4-enopyranuronate degradation	5	5	1
mannitol cycle	5	4	1
superpathway of (R,R)-butanediol biosynthesis	5	4	1
starch biosynthesis	10	6	2
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	2	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	2	2
superpathway of thiamine diphosphate biosynthesis II	11	7	2
methylgallate degradation	6	3	1
arsenate detoxification I	6	3	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
thiazole component of thiamine diphosphate biosynthesis I	6	2	1
arsenic detoxification (plants)	6	2	1
molybdopterin biosynthesis	6	2	1
Fe(II) oxidation	6	2	1
superpathway of L-isoleucine biosynthesis I	13	13	2
chorismate biosynthesis I	7	7	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
L-glutamate and L-glutamine biosynthesis	7	4	1
protocatechuate degradation I (meta-cleavage pathway)	8	4	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	2	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
superpathway of L-threonine metabolism	18	11	2
allantoin degradation IV (anaerobic)	9	4	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of thiamine diphosphate biosynthesis I	10	5	1
superpathway of vanillin and vanillate degradation	10	5	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	2	1
chorismate biosynthesis II (archaea)	12	8	1
syringate degradation	12	4	1
arsenic detoxification (yeast)	12	3	1
superpathway of L-tryptophan biosynthesis	13	13	1
gluconeogenesis I	13	11	1
3-hydroxypropanoate cycle	13	8	1
glyoxylate assimilation	13	5	1
superpathway of aromatic amino acid biosynthesis	18	18	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
superpathway of the 3-hydroxypropanoate cycle	18	8	1
superpathway of chorismate metabolism	59	38	1